DPP7 p.Ser3=
c.9C>A · VCV3770659
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.354%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.27 | GERP -1.6 |
| Overall | ||
| CADD | 3.156 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.354%
European (non-Finnish) · 3,644/1,028,432 alleles
Filtering AF
0.345%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.341%
Overall
0.309%
4,033/1,304,054 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.354% | 282 |
| Remaining individualsnot grpmax-eligible | 0.345% | 290 |
| South Asian | 0.261% | 383 |
| Admixed American | 0.219% | 458 |
| Middle Eastern | 0.176% | 570 |
| African / African-American | 0.0557% | 1,794 |
| Finnishnot grpmax-eligible | 0.03% | 3,328 |
| East Asian | 0.00316% | 31,636 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- DPP7
- Protein
- p.Ser3=
- Coding
- c.9C>A
- MANE Select
- NM_013379
- Type
- single nucleotide variant
- Location
- chr9:137114705 (GRCh38)
- Gene constraint
- LOEUF 1.707 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.44 · 3 PDB
Similar variants
- DPP7 p.Arg17= Likely benign ★★ same type
- DPP7 c.322-1G>T Uncertain significance ★ same type
- DPP7 p.Ala118Gly Uncertain significance ★ ⚠ same type
- DPP7 p.Ala118Val Uncertain significance ★ ⚠ same type
- DPP7 p.Ala136Val Uncertain significance ★ ⚠ same type
- DPP7 p.Ala139Gly Uncertain significance ★ ⚠ same type
- DPP7 p.Ala13Val Uncertain significance ★ ⚠ same type
- DPP7 p.Ala158Asp Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dpp7-p-ser3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown